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At least 145 records · Page 8

State of the Art of Molecular Visualization in Immersive Virtual Environments

Abstract Visualization plays a crucial role in molecular and structural biology. It has been successfully applied to a variety of tasks, including structural analysis and interactive drug design. While some of the challenges in this area can be overcome with more advanced visualization and interaction techniques, others are challenging primarily due to the limitations of the hardware devices used to interact with the visualized content. Consequently, visualization researchers are increasingly trying to take advantage of new technologies to facilitate the work of domain scientists. Some typical problems associated with classic 2D interfaces, such as regular desktop computers, are a lack of natural spatial understanding and interaction, and a limited field of view. These problems could be solved by immersive virtual environments and corresponding hardware, such as virtual reality head‐mounted displays. Thus, researchers are investigating the potential of immersive virtual environments in the field of molecular visualization. There is already a body of work ranging from educational approaches to protein visualization to applications for collaborative drug design. This review focuses on molecular visualization in immersive virtual environments as a whole, aiming to cover this area comprehensively. We divide the existing papers into different groups based on their application areas, and types of tasks performed. Furthermore, we also include a list of available software tools. We conclude the report with a discussion of potential future research on molecular visualization in immersive environments.

97 MATHEMATICS AND COMPUTING↗

Rancor-HUNTER: A Virtual Plant and Operator Environment for Predicting Human Performance

Advances in simulation capabilities to model physical systems have outpaced the development of simulations for humans using those physical systems. There is an argument that the infinite span of potential human behaviors inherently render human modeling more challenging than physical systems. Despite this challenge, the need for modeling humans interacting with these complex systems is paramount. As technologies have improved, many of the failure modes originating from the physical systems have been solved. This means the overall proportion of human errors has increased, such that it is not uncommon to be the primary driver of system failure in modern complex systems. Moreover, technologies such as automated systems may introduce emerging contexts that can cause new, unanticipated modes of human error. Therefore, it is now more important than ever to develop models of human behavior to realize overall system error reductions and achieve established safety margins. To support new and novel concepts of operations for the anticipated wave of advanced nuclear reactor deployments, human factors and human reliability analysis researchers need to develop advanced simulation-based approaches. This talk presents a simulation environment suitable to both collect data and then perform Monte Carlo simulations to evaluate human performance and develop better models of human behavior. Specifically, the Rancor Microworld Simulator models a complex energy production system in a simplified manner. Rancor includes computer-based procedures, which serve as a framework to automatically classify human behaviors without manual, subjective experimenter coding during scenarios. This method supports a detailed level of analysis at the task level. It is feasible for collecting large sample sizes required to develop quantitative modelling elements that have historically challenged traditional full-scope simulator study approaches. Additionally, the other portion of this experimental platform, the Human Unimodel for Nuclear Technology to Enhance Reliability (HUNTER), is presented to show how the collected data can be used to evaluate novel scenarios based on the contextual factors, or performance shaping factors, derived from Rancor simulations. Rancor-HUNTER is being used to predict operator performance with new procedures, such as results from control room modernization or new-build situations. Rancor-HUNTER is also proving a useful surrogate platform to model human performance for other complex systems.

99 GENERAL AND MISCELLANEOUS↗

SAM-ML: Integrating data-driven closure with nuclear system code SAM for improved modeling capability

Advanced reactors often involve complicated thermal-fluid (T-F) phenomena. Modeling such phenomena with the traditional one-dimensional (1-D) system code is a challenging task. The System Analysis Module (SAM), a modern nuclear system code, has developed a coarse mesh multi-dimensional (multi-D) flow model to capture the spatial effect of T-F phenomena in advanced reactors. As a coarse mesh solver, constitutive relations are required for SAM's multi-D model for unresolved fine-scale physics, such as turbulence. Here this work presents a novel approach that integrates neural networks as data-driven closure for SAM's multi-D flow model. The data-driven closure is trained with fine-resolution data to ensure its accuracy while maintaining a coarse mesh setup to ensure its efficiency and consistency with SAM. We demonstrate the applicability of this SAM-ML capability in an open volume thermal stratification problem, where a neural network model serves as the eddy viscosity closure. A customized interface between the neural network and SAM is developed to ensure flexible and efficient data exchange. The SAM-ML results demonstrate superior performance compared to SAM's built-in zero-equation eddy viscosity closure. The case study shows that although the generalization capability of the data-driven closure still needs to be improved for different transient case or different geometric setup, SAM -ML demonstrates good potential for challenging simulation problems with improved accuracy and computational efficiency.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Do-calculus enables estimation of causal effects in partially observed biomolecular pathways

Abstract Motivation Estimating causal queries, such as changes in protein abundance in response to a perturbation, is a fundamental task in the analysis of biomolecular pathways. The estimation requires experimental measurements on the pathway components. However, in practice many pathway components are left unobserved (latent) because they are either unknown, or difficult to measure. Latent variable models (LVMs) are well-suited for such estimation. Unfortunately, LVM-based estimation of causal queries can be inaccurate when parameters of the latent variables are not uniquely identified, or when the number of latent variables is misspecified. This has limited the use of LVMs for causal inference in biomolecular pathways. Results In this article, we propose a general and practical approach for LVM-based estimation of causal queries. We prove that, despite the challenges above, LVM-based estimators of causal queries are accurate if the queries are identifiable according to Pearl’s do-calculus and describe an algorithm for its estimation. We illustrate the breadth and the practical utility of this approach for estimating causal queries in four synthetic and two experimental case studies, where structures of biomolecular pathways challenge the existing methods for causal query estimation. Availability and implementation The code and the data documenting all the case studies are available at https://github.com/srtaheri/LVMwithDoCalculus. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

Big Data Analysis of Massive PMU Datasets: A Data Platform Perspective

The discovery of `event signatures' and useful insights from very large historical Phasor Measurement Unit (PMU) datasets is predicated on offline Big Data analysis approaches that rely on the generation of predictive features on a massive scale. This paper presents lessons learned from a data platform perspective towards reducing barriers to adoption of Big Data analytics against a real dataset of almost half a trillion data points drawn from over 400 PMUs distributed across the North American power grid. We demonstrate software abstractions and targeted performance optimizations that can lead to significant productivity gains for power systems researchers seeking to perform offline exploratory temporal analysis and modeling tasks, with a focus on feature generation. We describe how our optimized approach goes beyond a naive application of mainstream Big Data technologies, enabling feature generation tasks, that previously took days or even weeks, to now be completed in just a few hours.

Kumar, Vijay S.↗

wastewater_virus

This repo contains software used to clean and assemble high-throughput sequencing data containing viruses. The input is raw illumina sequencing reads and the output is a database of high-quality viral genomes. The specific application is to wastewater viral concentrates but it is not restricted to that sample type. The software is composed of Nextflow workflows and a set of custom Python and bash scripts that call publicly available bioinformatics tools to accomplish obvious tasks in data analysis in a high performance computing environment. For detailed information, please see the repo's README file.

Kantor, Rose [Lawrence Livermore National Laborato↗

Gamma-Ray Transient Network Science Analysis Group Report

The Interplanetary Network (IPN) is a detection, localization and alert system that utilizes the arrival time of transient signals in gamma-ray detectors on spacecraft separated by planetary baselines to geometrically locate the origin of these transients. Due to the changing astrophysical landscape and the new emphasis on time domain and multi messenger astrophysics (TDAMM) from the Pathways to Discovery in Astronomy and Astrophysics for the 2020s , this Gamma-ray Transient Network Science Analysis Group was tasked to understand the role of the IPN and high-energy monitors in this new era. The charge includes describing the science made possible with these facilities, tracing the corresponding requirements and capabilities, and highlighting where improved operations of existing instruments and the IPN would enhance TDAMM science. While this study considers the full multiwavelength and multimessenger context, the findings are specific to space-based high-energy monitors. These facilities are important both for full characterization of these transients as well as facilitating follow-up observations through discovery and localization. The full document reports the history of this field in Section 1, followed by our detailed analyses and findings in some 68 pages, providing a holistic overview of the role of the IPN and high-energy monitors in the coming decades.

79 ASTRONOMY AND ASTROPHYSICS↗

PROTEUS: Machine Learning Driven Resilience for Extreme-scale Systems

The objective of this project is to design, develop, and evaluate scalable software to enhance resilience, data checkpointing, program restart, and analysis. The proposed tasks are to 1) develop scalable machine learning techniques to learn temporal change patterns in a scalable and in-situ manner, and to minimize data movement and maximize learning locally closest to data; 2) design a concise data representation and indexing mechanism to capture the distribution of changes in data that can guarantee point-wise user-defined tolerable errors while reducing the data storage requirements by an order of magnitude or more; 3) develop data reduction techniques as library modules; 4) exploit local SSD for minimizing data movement in storage hierarchy; 5) develop anomaly detection algorithms that can predict corruptions based on learning of emerging patterns; 6) develop software libraries to be incorporated within widely used data formats and APIs; and 7) evaluate the proposed software using DOE scientific applications. The outcomes of the proposed work are to satisfy many synergistic data reduction and resilience requirements for large-scale data intensive applications executed on extreme-scale computing systems. The developed mechanism for error-bound data approximation is directly applicable to existing scientific applications. Through machine learning from historical events and change distribution, this work will enable anomaly detection for DOE computer facility.

97 MATHEMATICS AND COMPUTING↗

ExaWorks software development kit: a robust and scalable collection of interoperable workflows technologies

Scientific discovery increasingly requires executing heterogeneous scientific workflows on high-performance computing (HPC) platforms. Heterogeneous workflows contain different types of tasks (e.g., simulation, analysis, and learning) that need to be mapped, scheduled, and launched on different computing. That requires a software stack that enables users to code their workflows and automate resource management and workflow execution. Currently, there are many workflow technologies with diverse levels of robustness and capabilities, and users face difficult choices of software that can effectively and efficiently support their use cases on HPC machines, especially when considering the latest exascale platforms. We contributed to addressing this issue by developing the ExaWorks Software Development Kit (SDK). The SDK is a curated collection of workflow technologies engineered following current best practices and specifically designed to work on HPC platforms. We present our experience with (1) curating those technologies, (2) integrating them to provide users with new capabilities, (3) developing a continuous integration platform to test the SDK on DOE HPC platforms, (4) designing a dashboard to publish the results of those tests, and (5) devising an innovative documentation platform to help users to use those technologies. Our experience details the requirements and the best practices needed to curate workflow technologies, and it also serves as a blueprint for the capabilities and services that DOE will have to offer to support a variety of scientific heterogeneous workflows on the newly available exascale HPC platforms.

97 MATHEMATICS AND COMPUTING↗

Load Composition Analysis in Support of the NERC Load Modeling Task Force. 2019-2020 Field Test of the Composite Load Model

In 2015, NERC’s reliability standards were revised to require the use of dynamic load models in transmission planning studies. To comply with the standards, planners must use load models that explicitly represent the dynamic behavior of the different constituents of load at each load bus within their transmission planning models. The most important of these constituents are motor-driven and power electronics-based loads. Collectively, these representations are known as composite load models. In anticipation of the compliance date for the new standards, NERC’s Load Modeling Task Force (LMTF), in 2019, initiated a field test of composite load models involving the regional reliability planning entities. In support of the field test, DOE and BPA researchers developed region-specific composite load models that could be assigned to each non-industrial load bus in the planning models for each of the North American interconnections. Separate models were developed for each hour of a summer peak day, a winter peak day, and a spring light-load day. This report is the technical documentation for the load composition analysis that was conducted to develop these non-industrial composite load models.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Stakeholder Analysis Technical Report for CarbonSAFE Illinois -- Macon County (Task 3)

Stakeholder engagement is considered a critical component for successful deployment of Carbon Capture Utilization and Storage (CCUS). Engagement builds awareness and understanding of the implications, both local and global, that deploying this technology entails. The CarbonSAFE Illinois – Macon County project presents unique challenges for engaging stakeholders as they have various and diverse options and perspectives that vary in influence and personal importance.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Task 12 Sustainability - Methodological Guidelines on Net Energy Analysis of Photovoltaic Electricity (2nd Edition)

Net Energy Analysis (NEA) is a structured, comprehensive method of quantifying the extent to which a given energy source is able to provide a net energy gain (i.e., an energy surplus) to the end user, after accounting for all the energy losses occurring along the chain of processes that are required to exploit it (i.e., for its extraction, processing and transformation into a usable energy carrier, and delivery to the end user), as well as for all the additional energy 'investments' that are required in order to carry out the same chain of processes. However, this general framework leaves the individual practitioner with a range of choices that can affect the results and thus, the conclusions of a NEA study. The current IEA PVPS guidelines were developed to provide guidance on assuring consistency, balance, and quality to enhance the credibility and reliability of the results from photovoltaic (PV) NEAs. The guidelines represent a consensus among the authors - PV NEA experts in North America and Europe - for assumptions made on PV performance, process inputs and outputs, methods of analysis, and reporting of the results. Guidance is given on photovoltaic-specific parameters used as inputs in NEA and on choices and assumptions in inventory data analysis and on implementation of modelling approaches. A consistent approach towards system modelling, the functional unit, the system boundaries and allocation aspects enhance the credibility of PV electricity NEA studies and enables balanced NEA-based comparisons. Specifically, "apples-to-oranges" comparisons of different energy carriers (e.g., fuels vs. electricity) are not methodologically sound and are to be avoided in all cases; also, any comparison across renewable and non-renewable electricity generation technologies must clearly point out the intrinsically short-term nature of the NEA viewpoint, which does not capture the long-term sustainability implications of renewable vs. non-renewable primary energy harvesting and use: non-renewable primary energy resources are depleted and finally exhausted (irrespective of the size of the EROI), while renewable primary energy resources are not. This document provides an in-depth discussion of a common metric of NEA, namely the energy return on investment (EROI), and how this is to be interpreted vis-a-vis the deceptively similar-sounding metrics in the field of Life Cycle Assessment (LCA): cumulative energy demand (CED) and non-renewable cumulative energy demand (nr-CED) per unit output. Specifically, a number of key differences are highlighted between these metrics as applied to electricity production systems, which are listed in Table S-1.

14 SOLAR ENERGY↗

Demystifying the Resilience of Large Language Models: An End-to-End Perspective

Deep neural networks are known to be resilient to random bit-wise faults in their parameters. However, this resilience has primarily been established through evaluations of classification models. The extent to which this claim holds for large-language models remains underexplored. In this work, we conduct an extensive measurement study on the impact of random bitwise faults in commercial-scale language models. We perform an in-depth analysis of the resulting generation outputs. We first expose that these language models are not truly resilient to random bit-flips. While aggregate metrics such as accuracy may suggest resilience, an in-depth inspection of the generated outputs shows significant degradation in text quality. Our analysis also shows that tasks requiring more complex reasoning suffer more from performance and quality degradation. Moreover, we extend our analysis to models with augmented reasoning capabilities, such as Chain-of-Thought or Mixture of Experts architectures, and characterize their failure scenarios under random bit-flips.

Sun, Yu↗

Semi-Annual Report for Modular Integrated Gas High Temperature Reactor Development during Performance Period October 2021 - March 2022

Modular Integrated Gas High Temperature Reactor (MIGHTR) is being designed by a multidisciplinary team of nuclear, mechanical, and structural engineers under the support of a DOE-NE Advanced Reactor Demonstration Program’s Advanced Reactor Concepts-20 (ARC-20) award. The objective of this ARC-20 project is to deliver a conceptual design for the proposed MIGHTR in 3 years and support its commercialization as a safe and low-cost HTGR. Argonne National Laboratory is responsible for the design and analysis of the reactor cavity cooling system (RCCS) as a safety system for passive decay heat removal of the reactor concept. Work performed by Argonne also includes the thermal hydraulics analysis of the primary heat transport system including reactor pressure vessel (RPV) internals for normal operation, shutdown, and accident conditions. This first semi-annual report summarizes the progress made at Argonne on the two tasks since the start of the project. For the RCCS design task, high-level design work was performed including identification of design requirements for the conceptual MIGHTR RCCS and initial design calculations. The baseline dimensions of the MIGHTR RCCS were derived from scoping analysis results and preliminary steady state performance was estimated. At the initial stage of the primary system analysis task, the primary system thermal fluids model for the MIGHTR core was outlined to use a simplified two-dimensional model to predict the temperature distribution and coolant pressure losses in the fuel assembly blocks.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Big Adaptive Rotor Phase I (Final Report)

The Big Adaptive Rotor (BAR) project was initiate by DOE in 2018 with the goal of identifying novel technologies that can enable large (>100m) blades for low specific power (SP) turbines. Five distinct tasks were completed to achieve this goal: 1. Assess trends, impacts, and value of low-SP turbines, 2. Wind turbine blade cost reduction roadmap study, 3. Research and Development (R&D) opportunity screening, 4. Detailed design and analysis, and 5. Low-cost carbon fiber. These tasks were completed by the national lab team consisting of Sandia National Laboratories (SNL), the National Renewable Energy Laboratory (NREL), and Lawrence Berkeley National Laboratory (LBNL). The objective of Task 1 was to assess the historical trends of low-SP of onshore deployments, and to assess the impact and value of low-SP turbines. Analysis under this task showed that there is significant value for low-SP turbines, especially in markets where there is a higher saturation of wind energy on the grid. This has to do with the fact that low-SP turbines have increased capacity factors, and can contribute more reliable energy to the grid, even in lower wind conditions. This bodes well as higher renewable scenarios are likely in the coming years. Task 2 was a detailed analysis on the logistical challenges of deploying very large (>100m) onshore blade. This work was completed by experts at DNV-GL. The report looked at various ways to get around the current transportation constraints which are estimated to be around 75m in length. The report concluded that there are viable solutions to this issue including: segmented blades (which the industry is already pursuing), lighter than air (LTA) transportation, on-site manufacturing, and controlled bending of blades on rail. The final option was recommended for further analysis and study by DOE and the national labs because keeping a single piece blade reduces manufacturing and operations and maintenance (O&M) costs. Task 3 focused on identifying novel concepts that are capable of enabling a cost effective 5MW 206m rotor for onshore deployment. The findings from the first two tasks were considered in the analysis, in that the concepts identified must be able to overcome the transportation logistics challenges. Around 20 concepts were identified and evaluated by experts within the industry. Additionally, science and engineering challenges were identified for each concept. Based on these evaluations six concepts were deemed the most impactful and were selected for further analysis in Task 4. The concepts were: highly flexible rail transportable blades, downwind rotors, distributed aerodynamic control (DAC) devices, inflatable blade, bi-wing blade, and 4/5 bladed rotors. Task 4 conducted detailed design, optimization, and analysis on the selected BAR concepts. A modeling gaps analysis was conducted, and modeling improvements were implemented that allowed for the study and design of the novel concepts. The BAR team established a set of baseline designs by which to compare the selected designs through a technoeconomic analysis. It was found that the highly flexible rail transportable blade, the downwind rotor, and the DAC devices have the most promise to deliver the BAR targets. A Phase II for BAR has been proposed to further mature these concepts and address the open science and engineering challenges identified in Task 3. Task 5 conducted research on optimized carbon fiber materials that were used throughout the BAR Phase I project. Overall, the BAR project has identified low-SP turbines as important to continued LCOE reductions for onshore turbines. Furthermore, the project has identified viable solutions to the technical and logistical challenges to realizing these goals. The most promising technologies that were identified in Phase I of the project will be further matured and de-risked in Phase II of the BAR project.

17 WIND ENERGY↗

MRCI Subtask 2.4/2.5: Regional/Subregional Analysis and Risk Assessment Final Technical Summary Report

The objective of the Midwest Regional Carbon Initiative (MRCI) project is to implement a collaborative Regional Initiative (RI) to accelerate the deployment of carbon capture, and storage (CCS) in the Midwest-Northeastern quadrant of the United States. This report is a Technical Summary report describing work performed on Tasks 2.4 (Conducting Regional/Subregional Analysis) and 2.5 (Assessing and Managing Risk) during the MRCI project. In Task 2.4, detailed numerical reservoir simulation models were developed for selected carbon storage (CS) systems identified under Task 2.1 (Battelle, 2021a) in the MRCI study area. The objective of Task 2.4 is to demonstrate a dynamic modeling methodology for evaluating the suitability of the (selected) CS systems in the MRCI region for hosting a commercial-scale storage project. In this study, CO2 injectivity was evaluated for different CS systems with an annual injection rate of 1 million metric tonnes (MMT) of CO2 considered as the minimum requirement for a commercial scale project. The objective of Task 2.5 is to assess key risks associated with storing CO2 in the different CS systems across the MRCI region and to demonstrate a method(s) for assessing these risks that may be used by developers of future CO2 storage projects in the region. The risk analysis was limited to evaluating two types of leakage risks (i.e., wellbore leakage, flow across unfractured caprock) at three modeled sites considered in Task 2.4.

MRCI,Report,Summary,Technical Challenges,dynamic m↗

SMART Task 6: Evaluation of the Costs of Geologic CO2 Storage for the Illinois Basin Decatur Project Site Using the NRAP/SMART Technoeconomic and Liability Evaluation for Storage (TALES) Model

This is a presentation featuring an analysis related to SMART Task 6 in which CO2 storage costs are presented. The National Energy Technology Laboratory has developed the NRAP/SMART Technoeconomic and Liability Evaluation for Storage (TALES) model to provide quantitative cost-based insights to support developers planning CO2 injection and storage projects. TALES calculates the revenues, costs, and financial performance of candidate CO2 saline storage project based on site-specific activity costs and financial parameters. TALES is being integrated as a module pertaining to storage cost as part of the broader SMART Visualization and Decision Support Platform (SVDSP). In this study, the TALES model was applied using real activity cost data associated with the development and operations at the Illinois Basin Decatur Project (IBDP) CO2 storage project site. Scenario analysis was implemented in which crucial operational and cost attributes were varied and the associated cost implications observed. Key results data and project cost summary metrics like first-year breakeven price of CO2 ($/tonne) and net present value (NPV) are presented in similar fashion to how they will appear in the SVDSP.

Vikara, Derek↗